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change phase diffusion calc.
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Schaudge committed Sep 9, 2024
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Expand Up @@ -841,7 +841,7 @@ static Map<VariantContext, Triple<Integer, Integer, PhaseGroup>> constructPhaseS
final boolean compIsOnAllAltHaps = haplotypesWithComp.size() == totalAvailableHaplotypes;
final Sets.SetView<Haplotype> intersectionHaplotype = Sets.intersection(haplotypesWithCall, haplotypesWithComp);
final int phaseReadsCount = intersectionHaplotype.stream().mapToInt(Haplotype::getWeakness).max().orElse(0);
final double phaseDiffusionRate = Math.pow(1.1 * Math.log10(Math.min(callDepth, compDepth)), 2) + 5;
final double phaseDiffusionRate = 2 * Math.log10(Math.min(callDepth, compDepth)) + 1;

// For some high frequency complex long indels, that many reads not coverage the whole indels completely,
// and variants will dispatch to different haplotypes, so we relax the conditions for phase set combination!
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